#!usr/bin/perl -w

use strict;

die "format:\nsam1\tabsolute-pathway\nsam2\tabsolute-pathway\nusage:perl $0 <clw.fa.list> \n" unless @ARGV == 1;

open B,$ARGV[0];
my $shell2="pop_kaks";
mkdir $shell2 unless (-d $shell2);
while(<B>){
    chomp;my @a=split /\s+/;
    my $shell3="pop_kaks/".$a[0];
    mkdir $shell3 unless (-d $shell3);
    open SUB,">pop_kaks/$a[0]/codeml.ctl";
    print SUB "seqfile = $a[1]            * sequence data filename
    treefile = test.tre           * tree structure file name
    outfile =  $a[0].mlc.dN.dS.txt         * main result file name

    noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
    verbose = 1  * 0: concise; 1: detailed, 2: too much
    runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
    * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

    seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
    CodonFreq = 2  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table

    *        ndata = 10
    clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
    aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
    aaRatefile = dat/jones.dat  * only used for aa seqs with model=empirical(_F)
    * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

    model = 0
    * models for codons:
    * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
    * models for AAs or codon-translated AAs:
    * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
    * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

    NSsites = 0 3 7 8 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
    * 5:gamma;6:2gamma;7:beta;8:beta&w;9:beta&gamma;
    * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
    * 13:3normal>0

    icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
    Mgene = 0
    * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
    * AA: 0:rates, 1:separate

    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
    kappa = 2  * initial or fixed kappa
    fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate
    omega = .4 * initial or fixed omega, for codons or codon-based AAs

    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
    alpha = 0  * initial or fixed alpha, 0:infinity (constant rate)
    Malpha = 0  * different alphas for genes
    ncatG = 4  * # of categories in dG of NSsites models

    getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
    RateAncestor = 1  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

    Small_Diff = .5e-6
    cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
    *  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
    method = 0  * Optimization method 0: simultaneous; 1: one branch a time

    * Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
    * 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
    * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
    * 10: blepharisma nu.
    * These codes correspond to transl_table 1 to 11 of GENEBANK.\n";
    close SUB;
}
close B;
